Throughout this application various publications are referenced, many in parenthesis. Full citations for these publications are provided at the end of the Detailed Description of the Invention. The disclosures of these publications in their entireties are hereby incorporated by reference in this application.
Interferons ("IFNs") are a family of cytokines (Henco et al. 1985; Dron and Tovey 1992) with a variety of biological activities (Pestka et al. 1987 and Baron et al. 1992). They are named for their originally discovered activity of interfering with the infection of cells by virus (Issacs and Lindenmann 1957). Their use in the treatment of tumors is derived primarily from their ability to inhibit the growth of cells and to modulate cellular differentiation (Gutterman 1994). They are also known to affect every component of the immune system (Dianzani 1992), and long-term IFN-.alpha. therapy has induced systemic autoimmunity (Tolaymat et al. 1992, Wandl et al. 1992, Skurkovich et al. 1993, Stewart et al 1993, Paul and Seder 1994, and Schattner 1994). The mechanism for this is, in part, mediated through the induction of other cytokines that also act to modulate the immune system (Hooper 1994).
The biological activities of IFNs and other cytokines are mediated through binding and activation of specific receptors of the cytokine receptor superfamily (Ihle and Kerr 1995). The cell response occurs by the phosphorylation of selected signal transducers and activators of transcription ("STAT") proteins by specific Jak kinases (Heim et al. 1995). The phosphorylated proteins form complexes, which migrate to the nucleus, bind to a specific promoter (interferon-stimulated response element for IFN-.alpha.s), and activate the corresponding genes. Specificity of cell activation is attributed to the particular STAT proteins that are phosphorylated. These are determined by the STAT's particular phosphotyrosine-binding domain for the receptor rather than by the Jak kinases that associate with the receptor (Heim et al. 1995). Many cytokines use the same STAT proteins in their intracellular activation pathways. This may suggest that individually or in combination cytokines may activate some of the same genes to induce at least some of the same proteins.
The most studied IFN-induced proteins, such as Mx, Pl/eIF-2.alpha. protein kinase, and 2'5'-oligo(A) synthetases, are those believed to be necessary for establishing an antiviral state (Staeheli 1990 and Sen and Ransohoff 1993). Cytokine tumor necrosis factor is also known to be induced by IFN-.alpha. (Hooper 1994). Most other induced proteins have been identified on two-dimensional gels only as protein spots (Gustafsson et al. 1982, Leanderson et al. 1982, and Beresini et al. 1988). Their functions and biological significances are unknown. Many of these proteins are synthesized constitutively at low levels, and they are enhanced in response to both .alpha.- and .gamma.-IFNs (Staeheli 1990, Sen and Ransohoff 1993, and Beresini et al. 1988).
Lupus inclusions ("LI") (also called tubuloreticular structures or tubuloreticular inclusions) are IFN-.alpha.-induced (Rich 1981) abnormal cytoplasmic structures of unknown function that resemble myxovirus by ultramorphology (see, for example FIG. 1 of Gyorkey et al. 1969). They are membrane delimited complexes of tubular structures, 20 to 28 nm in diameter, and are characterized by their unique ultrastructural appearance. LI are composed of ribonucleoprotein and membrane complexes with carbohydrate and no DNA. They form in a restricted region of the endoplasmic reticulum ("ER") that makes contact with adjacent regions of the outer nuclear envelope and the Golgi apparatus (Rich et al. 1992). As indicated above, the function of LI is not known. However, the ER location of LI suggests that they may affect the established ER functions of membrane biogenesis, the trafficking of proteins to the plasma membrane or to cytoplasmic vesicles, or the processing of proteins for secretion.
LI formation in endothelial and mononuclear cells is a prognostic marker for disease progression in individuals with acquired immune deficiency syndrome ("AIDS") (Feremans et al. 1988, Orenstein et al. 1985, and Sidhu 1985), and their incidence reflects the disease activities of individuals with systemic lupus erythematosus ("SLE") (Rich et al. 1986). These structures are not detected in the cells of healthy individuals (Rich et al. 1986). An unusual acid-labile IFN-.alpha. is present continuously in the circulation of individuals with SLE and AIDS (De Stefano et al. 1982 and Preble et al. 1982). This is in contrast to a typical viral infection, in which IFN-.alpha. is produced as a burst for a 24 h period only. The unusual acid-labile IFN-.alpha. in sera from individuals with SLE and AIDS has an extraordinary ability to induce LI (Rich et al 1986 and Rich and Owens 1984). LI are known to be products of normal cells abnormally stimulated with IFN-.alpha. because peripheral blood mononuclear cells from healthy adult Red Cross blood donors (Rich et al. 1983) and umbilical-cord bloods from routine births (Rich and Gibbons 1990) form LI when cultured with IFN-.alpha..
Because of their association with immunodeficiency and autoimmune diseases, such as SLE and AIDS, LI or LI associated proteins have been investigated extensively for monitoring the progression of these diseases and the effectiveness of treatment regimens as well as for therapeutic activity. However, detection of LI is complicated by their small size and by the need to detect their presence visually. As to proteins uniquely associated with LI, though some are presently known, they have not been characterized in terms of their amino acid and nucleotide sequence. Because the nucleotide sequence encoding these proteins has heretofore been unknown, isolation of these proteins in useful quantities has not been achieved, and the use of the knowledge of such sequence data has not been possible.
A need exists, therefore, for the determination of the nucleotide and amino acid sequences of proteins induced by interferon-.alpha. or uniquely associated with LI. The present invention is directed to meeting this need.